| Variant ID: vg0213595540 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 13595540 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )
CCGGTCAGTTCAGTCGTGCAGGTTTGGACCATTGAGGAATCGGTCAGTTGAATCAGAAAGGAACAATGCAGTGTGCAAATCAGTCAGACCGCCTGCCAGC[C/T]
CCAGTTTTTCTTTCTAGCCATCCCAGAATCTCGGGACGAGATTCCTGTAAGGGGGGTAGATTTGTAACGCCCCGATTTTCGTTCGGGATTAAAAATCAAT
ATTGATTTTTAATCCCGAACGAAAATCGGGGCGTTACAAATCTACCCCCCTTACAGGAATCTCGTCCCGAGATTCTGGGATGGCTAGAAAGAAAAACTGG[G/A]
GCTGGCAGGCGGTCTGACTGATTTGCACACTGCATTGTTCCTTTCTGATTCAACTGACCGATTCCTCAATGGTCCAAACCTGCACGACTGAACTGACCGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.00% | 0.10% | 3.03% | 5.88% | NA |
| All Indica | 2759 | 85.00% | 0.00% | 4.97% | 10.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 96.30% | 1.90% | 1.49% | 0.37% | NA |
| Indica I | 595 | 77.60% | 0.00% | 6.89% | 15.46% | NA |
| Indica II | 465 | 76.80% | 0.20% | 5.81% | 17.20% | NA |
| Indica III | 913 | 93.00% | 0.00% | 3.07% | 3.94% | NA |
| Indica Intermediate | 786 | 86.10% | 0.00% | 5.22% | 8.65% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0213595540 | C -> T | LOC_Os02g22810.1 | downstream_gene_variant ; 2386.0bp to feature; MODIFIER | silent_mutation | Average:46.027; most accessible tissue: Minghui63 flower, score: 65.9 | N | N | N | N |
| vg0213595540 | C -> T | LOC_Os02g22810-LOC_Os02g22820 | intergenic_region ; MODIFIER | silent_mutation | Average:46.027; most accessible tissue: Minghui63 flower, score: 65.9 | N | N | N | N |
| vg0213595540 | C -> DEL | N | N | silent_mutation | Average:46.027; most accessible tissue: Minghui63 flower, score: 65.9 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0213595540 | NA | 4.70E-07 | mr1328 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0213595540 | NA | 4.14E-06 | mr1574 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0213595540 | NA | 7.38E-13 | mr1612 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0213595540 | NA | 1.80E-08 | mr1952 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |